Contact patterns between helices and strands of sheet define protein folding patterns
Contact patterns between helices and strands of sheet define protein folding patterns
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DOI：
10.1002/prot.21241
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发表时间：
2007-03-01
影响因子：
2.9
通讯作者：
Lesk, Arthur M.
中科院分区：
文献类型：
--
作者：
Kamat, Akhil P.;Lesk, Arthur M.
比较和分类蛋白质折叠模式可以组织已知的结构并枚举可能的蛋白质结构模式，包括尚未观察到的蛋白质结构模式。我们根据二级结构（螺旋和片链）的顺序和接触模式，以简洁的画面表示形式捕捉蛋白质折叠模式的本质。这些画面对于人类和计算机来说都是可以理解的。他们提供了一个源自蛋白质数据库的数据库，可用于蛋白质结构的研究。使用该数据库，我们：(i) 确定了来自 ASTRAL 的一组无偏差蛋白质结构域中二级结构接触的统计特性，(ii) 观察到在 98% 的情况下，该表格是 SCOP 中分类的折叠模式的忠实表示，(iii) 证明蛋白质的局部结构在很大程度上表明了其完整的折叠拓扑，以及 (iv) 研究了该表示在折叠识别中的使用。
Comparing and classifying protein folding patterns allows organizing the known structures and enumerating possible protein structural patterns including those not yet observed. We capture the essence of protein folding patterns in a concise tableau representation based on the order and contact patterns of secondary structures: helices and strands of sheet. The tableaux are intelligible to both humans and computers. They provide a database, derived from the Protein Data Bank, mineable in studies of protein architecture. Using this database, we have: (i) determined statistical properties of secondary structure contacts in an unbiased set of protein domains from ASTRAL, (ii) observed that in 98% of cases, the tableau is a faithful representation of the folding pattern as classified in SCOP, (iii) demonstrated that to a large extent the local structure of proteins indicates their complete folding topology, and (iv) studied the use of the representation for fold identification.